Archive for the 'Data' category

A graphical representation of my frustration

Sep 17 2015 Published by under Data

I'm working on making figures for a paper that I walked into and have done some work to wrap up the study. I'm currently going batty digging through old files to find the raw files that were used to create graphs that apparently only exist in powerpoint files. These things are spread out to the four corners of the earth and its getting really annoying. Some of the files are in prism, some are in excel, some are in jmp, its getting crazy. If I make a figure I keep the raw data in excel but tend to make the polished figure in prism so its sitting there waiting to go into a publication.

Do you guys have a standard for graphs and how you want to see them?

2 responses so far

A Discourse on Electronic Lab Notebooks

Sep 11 2015 Published by under Data, Lab, Postdoc

Is anyone using an ELN system for their lab. I've been looking at a few, Evernote in particular, to help me keep my multiple projects organized? Didn't know if you found a helpful system or what difficulties you had in implementing this?

7 responses so far

On this day...DNA structure

Apr 25 2012 Published by under Data, Publishing

Today marks the 59 anniversary of the seminal paper from Watson and Crick describing the structure of DNA.  It is definitely worth re-reading.  I can't believe how short it is and how long Nature papers have become.


2 responses so far

Got Data???

Feb 28 2011 Published by under Data

Actually you've probably got too much and you probably don't have the time to sift through it, let alone store it in an organized fashion for perpetuity.  Data management is (at least for some of us) becoming almost as cumbersome as getting the damn stuff to begin with.  It would be great if we had a bioinformatician chained next to us at the bench so they could be analyzing and processing the data as we are creating it in real time.  And a few labs even do, but they are the serious outliers.  At best some of us are crunching our own numbers but the rest of us poor saps are having to hand off our data to others for this task and wait in queue.

Next where are we storing these vast quantities of digital data?  Are your universities and institutions setting up and running secure servers so that you data is at least protected and accessible to you let alone the public?  Do you have a mini-server or a more complicated RAID5 setup humming away in the corner of your lab?  Or are you the poor bastard whose data is only on the hard drive of your desktop that is infrequently if ever backed up?

I think a huge problem that is on the horizon, especially with doing research that is data intensive is:

-Where are we storing it?  Should we be dumping it all into government repositories like some folks stash their microarray data in GEO or Gene Expression Atlas.

-Should we be using a standardized format for data that we store?  Excel, ASCII, comma versus tab separated values?  Ugh!

-Do we do our own bioinformatics or just farm it out?  Before the rate limiting factor of some my research was doing the experiments.  Now its data processing and analysis.  A recent survey in Science showed that only 24% of respondents had the capability to do in-lab data analysis. 34% were using collaborators and 23% felt that they did not have the necessary skills to analyze their own data.

-Do we store published data on university servers which are more stable and kept current than those that exist in many lab currently?  And who the hell is going to pay for this?  80% of those surveyed said they did not have sufficient funding for data curation and 50% of the labs were keeping data archives on computers in their lab.  And as Dorothea has previously brought up, there is a general lack of research IT.

-What are our policies for data requests?  Should there be a standardized policy put forth by the NIH, universities or just leave it up to the individual lab?  Less than half of the labs that asked for data got it, with the other half only getting requests for published data fulfilled "sometimes."

We've got to tame this tiger before it gets too out of hand.

10 responses so far